import numpy as np
import pandas as pd
from sklearn.preprocessing import StandardScaler
import matplotlib.pyplot as plt
import seaborn as sns
%matplotlib inline
import warnings
warnings.filterwarnings('ignore')
import tensorflow as tf
from tensorflow import keras
import umap.umap_ as umap
%config InlineBackend.figure_format = 'svg'
np.random.seed(42)
pd.set_option('display.max_columns', None)
pd.set_option('display.max_rows', 100)
data=pd.read_csv('Preprocessed_DM_xx.csv')
np.random.seed(42)
data=data.sample(frac=1) #Shuffle the data set
np.random.seed(42)
HTN_indexes=data.loc[(data['Currently.taking.a.prescribed.medicine.to.lower.BP'] != 0) | (data['First.SYSTOLIC.reading'] >= 140) | (data['First.DIASTOLIC.reading'] >= 90) ].index.values
HTN_cols=np.zeros(data.shape[0])
HTN_cols[[HTN_indexes]]=1
data['HTN']=HTN_cols
data=data.drop(["First.SYSTOLIC.reading","First.DIASTOLIC.reading","Currently.taking.a.prescribed.medicine.to.lower.BP"], axis=1)
data=data.reset_index(drop=True)
data.columns
data=data.drop(["Hb_adjust_alt_smok","Second.SYSTOLIC.reading","Second.DIASTOLIC.reading","Third.SYSTOLIC.reading","Third.DIASTOLIC.reading","Hb_status","Glucose.level",'SBP_status'], axis=1)
data=data.loc[data['BMI'] != 99.99]
data=data.loc[data['Hemoglobin.level..g.dl...1.decimal.'] != 99.99]
data=data.loc[data['Currently.has.asthma'] != .5]
data=data.loc[data['Currently.has.thyroid.disorder'] != .5]
data=data.loc[data['Currently.has.heart.disease'] != .5]
data=data.loc[data['Currently.has.cancer'] != .5]
data=data.loc[data['DM_history'] == 1]
data=data.loc[data['Type.of.caste.or.tribe.of.the.household.head'] != 0]
data=data.loc[data['Time.to.get.to.water.source..minutes.'] != -1]
data=data.drop(["Unnamed: 0","DM_status","DM_history"], axis=1)
np.random.seed(42)
i=[x for x in range(10125)]
data.set_index(pd.Series(i), inplace=True) # Reset the index
Creating 2 new dataframes: "data_disease" with features related to disease and "data_others" with rest of the features
data_disease= data[['Currently.has.asthma',
'Currently.has.thyroid.disorder', 'Currently.has.heart.disease',
'Currently.has.cancer', 'Suffers.from.TB','HTN']]
data_others= data[['Drinks.alcohol', 'Smoking_stat','Has.refrigerator',
'Has.bicycle', 'Has.motorcycle.scooter', 'Has.car.truck', 'Owns.livestock..herds.or.farm.animals','Frequency.takes.milk.or.curd',
'Frequency.eats.pulses.or.beans',
'Frequency.eats.dark.green.leafy.vegetable', 'Frequency.eats.fruits',
'Frequency.eats.eggs', 'Frequency.eats.fish',
'Frequency.eats.chicken.or.meat', 'Frequency.eats.fried.food',
'Frequency.takes.aerated.drinks','Frequency.household.members.smoke.inside.the.house','Wealth.index',
'Highest.educational.level', 'Current.age','BMI','Hemoglobin.level..g.dl...1.decimal.','Time.to.get.to.water.source..minutes.', 'Household.head.s.religion', 'Sex', 'Type.of.place.of.residence', 'Household.structure',
'Type.of.caste.or.tribe.of.the.household.head','Type.of.cooking.fuel','Source.of.drinking.water']]
def feature_clustering(UMAP_neb,min_dist_UMAP, metric, data, visual):
import umap.umap_ as umap
np.random.seed(42)
data_embedded = umap.UMAP(n_neighbors=UMAP_neb, min_dist=min_dist_UMAP, n_components=2, metric=metric, random_state=42).fit_transform(data)
data_embedded[:,0]=(data_embedded[:,0]- np.mean(data_embedded[:,0]))/np.std(data_embedded[:,0])
data_embedded[:,1]=(data_embedded[:,1]- np.mean(data_embedded[:,1]))/np.std(data_embedded[:,1])
result = pd.DataFrame(data = data_embedded ,
columns = ['UMAP_0', 'UMAP_1'])
if visual==1:
sns.lmplot( x="UMAP_0", y="UMAP_1",data=result,fit_reg=False,legend=False,scatter_kws={"s": 3},palette=customPalette_set1) # specify the point size
#plt.savefig('clusters_umap_all.png', dpi=700, bbox_inches='tight')
plt.show()
else:
pass
return result
ord_list=['Drinks.alcohol', 'Smoking_stat','Has.refrigerator',
'Has.bicycle', 'Has.motorcycle.scooter', 'Has.car.truck', 'Owns.livestock..herds.or.farm.animals','Frequency.takes.milk.or.curd',
'Frequency.eats.pulses.or.beans',
'Frequency.eats.dark.green.leafy.vegetable', 'Frequency.eats.fruits',
'Frequency.eats.eggs', 'Frequency.eats.fish',
'Frequency.eats.chicken.or.meat', 'Frequency.eats.fried.food',
'Frequency.takes.aerated.drinks','Frequency.household.members.smoke.inside.the.house','Wealth.index',
'Highest.educational.level' ]
cont_list=['Current.age','BMI','Hemoglobin.level..g.dl...1.decimal.','Time.to.get.to.water.source..minutes.']
nom_list=['Household.head.s.religion', 'Sex', 'Type.of.place.of.residence', 'Household.structure',
'Type.of.caste.or.tribe.of.the.household.head','Type.of.cooking.fuel','Source.of.drinking.water']
def FDC(data,cont_list,nom_list,ord_list,cont_metric, ord_metric, nom_metric, drop_nominal, visual):
np.random.seed(42)
colors_set1 = ["lightcoral", "lightseagreen", "mediumorchid", "orange", "burlywood", "cornflowerblue", "plum", "yellowgreen"]
customPalette_set1 = sns.set_palette(sns.color_palette(colors_set1))
cont_df=data[cont_list]
nom_df=data[nom_list]
ord_df=data[ord_list]
cont_emb=feature_clustering(30,0.1, cont_metric, cont_df, 0) #Reducing continueous features into 2dim
ord_emb=feature_clustering(30,0.1, ord_metric, ord_df, 0) #Reducing ordinal features into 2dim
nom_emb=feature_clustering(30,0.1, nom_metric, nom_df, 0) #Reducing nominal features into 2dim
if drop_nominal==1:
result_concat=pd.concat([ord_emb, cont_emb, nom_emb.drop(['UMAP_1'],axis=1)],axis=1) #concatinating all reduced dimensions to get 5D embeddings(1D from nominal)
else:
result_concat=pd.concat([ord_emb, cont_emb, nom_emb],axis=1)
data_embedded = umap.UMAP(n_neighbors=30, min_dist=0.001, n_components=2, metric='euclidean', random_state=42).fit_transform(result_concat) #reducing 5D embeddings to 2D using UMAP
result_reduced = pd.DataFrame(data = data_embedded ,
columns = ['UMAP_0', 'UMAP_1'])
if visual==1:
sns.lmplot( x="UMAP_0", y="UMAP_1",data=result_reduced,fit_reg=False,legend=False,scatter_kws={"s": 3},palette=customPalette_set1) # specify the point size
plt.show()
#plt.savefig('clusters_umap_all.png', dpi=700, bbox_inches='tight')
else:
pass
return result_concat, result_reduced #returns both 5D and 2D embeddings
# applying Feature Distributed Clustering(FDC) on entire 10125 data with all features except disease features
entire_data_FDC_emb_five,entire_data_FDC_emb_two=FDC(data_others,cont_list,nom_list,ord_list,'euclidean','canberra','hamming',1,1)
def aglo_clustering(no_of_clusters, affinity, linkage, thirty_d_embedding, two_d_embedding,visual,pal):
np.random.seed(42)
from sklearn.cluster import AgglomerativeClustering
ag_cluster = AgglomerativeClustering(n_clusters=no_of_clusters,affinity=affinity,linkage=linkage)
clusters=ag_cluster.fit_predict(thirty_d_embedding)
(values,counts) = np.unique(clusters,return_counts=True)
two_d_embedding['Cluster'] = clusters
if visual==1:
sns.lmplot( x="UMAP_0", y="UMAP_1",
data=two_d_embedding,
fit_reg=False,
legend=True,
hue='Cluster', # color by cluster
scatter_kws={"s": 3},palette=pal) # specify the point size
plt.savefig('agglo_ref_30dim.png', dpi=700, bbox_inches='tight')
plt.show()
else:
pass
return two_d_embedding.Cluster.to_list(),counts
#setting color palette for visualization of clusters
colors_set1 = ['lightcoral','cornflowerblue','orange','mediumorchid', 'lightseagreen','olive', 'chocolate','steelblue']
customPalette_set1 = sns.set_palette(sns.color_palette(colors_set1))
#Applying clustering algorithm on FDC embedding from entire data
entire_data_cluster_list,entire_data_cluster_counts=aglo_clustering(4, "euclidean", "ward",data_others,entire_data_FDC_emb_two,1,customPalette_set1)
#Getting noise indices
non_noise_indices= np.where(np.array(entire_data_cluster_list)!=-1)
#Removing noise/outlires from FDC embeddings and from entire data
entire_data_FDC_emb_five= entire_data_FDC_emb_five.iloc[non_noise_indices]
entire_data_FDC_emb_two= entire_data_FDC_emb_two.iloc[non_noise_indices]
entire_data_cluster_list= np.array(entire_data_cluster_list)[non_noise_indices]
data_others= data_others.iloc[non_noise_indices]
#Creating new cloumn for storing cluster labels
data_others['cluster_labels']= entire_data_cluster_list
#getting binary representation for cluster labels
data_others= pd.get_dummies(data=data_others, columns=['cluster_labels'])
#Getting column names of encoded cluster labels
cluster_column_names=data_others.columns[-len(np.unique(entire_data_cluster_list)):].to_list()
#75% of entire data for training
np.random.seed(42)
data=data_others.sample(frac=0.75) # Training data
#Another 25% of entire data for validation
np.random.seed(42)
data_val=data_others.drop(data.index) # Validation data
#Dividing training data into three folds
np.random.seed(42)
df_1=data.sample(frac=0.33) #fold 1
df=data.drop(df_1.index)
df_2=df.sample(frac=0.51) #fold 2
df_3=df.drop(df_2.index) #fold 3
np.random.seed(42)
#Possible combinations of concating 2 folds for training and using remaining fold for testing
training_folds=[pd.concat([df_1,df_2],axis=0), pd.concat([df_2,df_3],axis=0), pd.concat([df_3,df_1],axis=0)]
testing_folds=[df_3,df_1,df_2]
def neural_network(n_features,hidden_dim1,hidden_dim2,out_emb_size,act1,act2,loss):
np.random.seed(42)
tf.random.set_seed(42)
model=keras.Sequential([
keras.layers.Dense(hidden_dim1,input_dim=n_features,activation=act1),
keras.layers.Dense(hidden_dim1,activation=act2),
keras.layers.Dense(out_emb_size)])
model.compile(optimizer="adam" ,
loss=loss,
metrics=['mse'])
return model
def cluster_incidence_matrix_mod(cluster_list_new):
np.random.seed(42)
matrix=np.zeros((len(cluster_list_new),len(cluster_list_new)))
for i in range(len(cluster_list_new)):
for j in range(len(cluster_list_new)):
if cluster_list_new[i]==cluster_list_new[j]:
matrix[i,j]=1
else:
pass
return matrix
#Function for decoding the encoded cluster labels
def label_decoder(label_dataframe):
label_array=np.array(label_dataframe)
decoded_labels=[]
for i in label_array:
max_val=np.argmax(i)
decoded_labels.append(max_val)
return decoded_labels
colnames=[]
for i in range(len(entire_data_FDC_emb_five.columns)):
colnames.append('c'+str(i+1))
np.random.seed(42)
count=0
fold_readings=[]
while count<3:
FDC_emb_five_train=entire_data_FDC_emb_five.loc[list(training_folds[count].index)] #3D FDC embedding of training folds from entire training data
FDC_emb_two_train=entire_data_FDC_emb_two.loc[list(training_folds[count].index)] #2D embedding of training folds from entire training data
FDC_emb_five_train.columns=colnames
#Thirty dimensional data of training fold as features_matrix(X_train)
features_matrix=np.array(training_folds[count].drop(cluster_column_names, axis=1,inplace=False)) #X_train
#three dimensional FDC embedding of training fold as target_matrix(y_train)
target_matrix=np.array(FDC_emb_five_train) #y_train
#Train a neural network to get five dimensional embedding
model_1=neural_network(len(features_matrix[0]),int(0.6*len(features_matrix[0])),int(0.36*len(features_matrix[0])),len(target_matrix[0]),"relu","sigmoid","mse")
history=model_1.fit(features_matrix,target_matrix,epochs=30,batch_size=8)
print('\n')
print('Training history across epochs for fold ',count+1)
plt.plot(history.history['mse'],'r')
plt.ylabel('mse')
plt.xlabel('epoch')
plt.show()
#Using same thirty dimensional features_matrix(X_train) from first neural network and encoded cluster labels of training fold as target_labels_matrix(y_train)
target_labels_matrix=np.array(training_folds[count].loc[:,cluster_column_names]) #y
#Train a neural network to get encoded cluster labels
model_2=neural_network(len(features_matrix[0]),int(0.6*len(features_matrix[0])),int(0.36*len(features_matrix[0])),len(target_labels_matrix[0]),"relu","softmax","mse")
history=model_2.fit(features_matrix,target_labels_matrix,epochs=30,batch_size=8)
print('\n')
print('Training history across epochs for fold ',count+1)
plt.plot(history.history['mse'],'r')
plt.ylabel('mse')
plt.xlabel('epoch')
plt.show()
#Decoding cluster labels of training fold
decoded_target_labels_matrix=label_decoder(target_labels_matrix)
#Actual encoded cluster labels of testing fold for metric calculation
ref_clusters=testing_folds[count].loc[:,cluster_column_names]
#Decoding encoded cluster labels of testing fold
decoded_ref_clusters=label_decoder(ref_clusters)
#predicting testing fold to get three dim embedding using trained model_1
testing_data=testing_folds[count].drop(cluster_column_names, axis=1,inplace=False)
predicted_5dim=pd.DataFrame(model_1.predict(testing_data), columns=colnames)
#UMAP on predicted 3D embedding
predicted_2dim=feature_clustering(30,0.01, "euclidean", predicted_5dim, 0)
#predicting testing fold to get encoded cluster labels using trained model_2
predicted_clusters=pd.DataFrame(model_2.predict(testing_data))
#Decoding predicted encoded cluster labels
decoded_predicted_clusters=label_decoder(predicted_clusters)
#concatinating training and predicted 3D embedding
concatenated_5dim=pd.concat([FDC_emb_five_train,predicted_5dim])
#UMAP on concatinated embedding
two_dim_viz=feature_clustering(30, 0.01, 'euclidean', concatenated_5dim, 0)
#Concatinating decoded cluster labels of training fold and predicted testing fold
concatenated_cluster_labels=np.concatenate([np.array(decoded_target_labels_matrix),np.array(decoded_predicted_clusters)+len(np.unique(decoded_target_labels_matrix))])
two_dim_viz['Cluster']= concatenated_cluster_labels
#Setting dark colors for training folds
darkerhues=['lightcoral','cornflowerblue','orange','mediumorchid', 'lightseagreen','olive', 'chocolate','steelblue']
colors_set2=[]
for i in range(len(np.unique(decoded_target_labels_matrix))):
colors_set2.append(darkerhues[i])
#Concatinating dark colors for training folds and corresponding light colors for testing folds
colors_set2=colors_set2+["lightpink", 'skyblue', 'wheat', "plum","paleturquoise", "lightgreen", 'burlywood','lightsteelblue']
print('Vizualization for FDC for training fold (shown in dark hue) '+str(count+1) + 'and predicted clusters from neural network on testing fold (shown in corresponding light hues) '+str(count+1))
#visualizing the clusters of both training and testing folds
sns.lmplot( x="UMAP_0", y="UMAP_1", data=two_dim_viz, fit_reg=False, legend=False, hue='Cluster', scatter_kws={"s": 3},palette=sns.set_palette(sns.color_palette(colors_set2)))
plt.show()
#Metric calculation
CIM_predicted=cluster_incidence_matrix_mod(np.array(decoded_predicted_clusters))#Cluster incidence metric for predicted clusters
CIM_reference=cluster_incidence_matrix_mod(np.array(decoded_ref_clusters))#Cluster incidence metric for reference clusters
Product=np.dot(CIM_predicted,CIM_reference)
cluster_incdences_in_data=np.sum(CIM_reference,axis=1)
mean_points_in_same_clusters=np.mean(np.diagonal(Product)/cluster_incdences_in_data)
fold_readings.append(mean_points_in_same_clusters*100)
print("Average percentage of patients belongs to the same cluster is: {}%".format(mean_points_in_same_clusters*100))
print('\n')
count+=1
print('\n')
print('\n')
Epoch 1/30 638/638 [==============================] - 1s 1ms/step - loss: 0.7376 - mse: 0.7376 Epoch 2/30 638/638 [==============================] - 1s 1ms/step - loss: 0.4387 - mse: 0.4387 Epoch 3/30 638/638 [==============================] - 1s 1ms/step - loss: 0.3622 - mse: 0.3622 Epoch 4/30 638/638 [==============================] - 1s 1ms/step - loss: 0.3286 - mse: 0.3286 Epoch 5/30 638/638 [==============================] - 1s 1ms/step - loss: 0.3076 - mse: 0.3076 Epoch 6/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2948 - mse: 0.2948 Epoch 7/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2838 - mse: 0.2838 Epoch 8/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2769 - mse: 0.2769 Epoch 9/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2704 - mse: 0.2704 Epoch 10/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2645 - mse: 0.2645 Epoch 11/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2602 - mse: 0.2602 Epoch 12/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2570 - mse: 0.2570 Epoch 13/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2522 - mse: 0.2522 Epoch 14/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2489 - mse: 0.2489 Epoch 15/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2454 - mse: 0.2454 Epoch 16/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2421 - mse: 0.2421 Epoch 17/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2394 - mse: 0.2394 Epoch 18/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2377 - mse: 0.2377 Epoch 19/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2354 - mse: 0.2354 Epoch 20/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2329 - mse: 0.2329 Epoch 21/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2313 - mse: 0.2313 Epoch 22/30 638/638 [==============================] - 1s 993us/step - loss: 0.2298 - mse: 0.2298 Epoch 23/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2271 - mse: 0.2271 Epoch 24/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2241 - mse: 0.2241 Epoch 25/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2216 - mse: 0.2216 Epoch 26/30 638/638 [==============================] - 1s 991us/step - loss: 0.2196 - mse: 0.2196 Epoch 27/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2171 - mse: 0.2171 Epoch 28/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2150 - mse: 0.2150 Epoch 29/30 638/638 [==============================] - 1s 1ms/step - loss: 0.2122 - mse: 0.2122 Epoch 30/30 638/638 [==============================] - 1s 981us/step - loss: 0.2090 - mse: 0.2090 Training history across epochs for fold 1
Epoch 1/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0831 - mse: 0.0831 Epoch 2/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0321 - mse: 0.0321 Epoch 3/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0264 - mse: 0.0264 Epoch 4/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0231 - mse: 0.0231 Epoch 5/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0219 - mse: 0.0219 Epoch 6/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0210 - mse: 0.0210 Epoch 7/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0202 - mse: 0.0202 Epoch 8/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0195 - mse: 0.0195 Epoch 9/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0191 - mse: 0.0191 Epoch 10/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0183 - mse: 0.0183 Epoch 11/30 638/638 [==============================] - 1s 1000us/step - loss: 0.0182 - mse: 0.0182 Epoch 12/30 638/638 [==============================] - 1s 992us/step - loss: 0.0179 - mse: 0.0179 Epoch 13/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0172 - mse: 0.0172 Epoch 14/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0173 - mse: 0.0173 Epoch 15/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0168 - mse: 0.0168 Epoch 16/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0167 - mse: 0.0167 Epoch 17/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0166 - mse: 0.0166 Epoch 18/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0163 - mse: 0.0163 Epoch 19/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0161 - mse: 0.0161 Epoch 20/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0160 - mse: 0.0160 Epoch 21/30 638/638 [==============================] - 1s 960us/step - loss: 0.0156 - mse: 0.0156 Epoch 22/30 638/638 [==============================] - 1s 968us/step - loss: 0.0155 - mse: 0.0155 Epoch 23/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0153 - mse: 0.0153 Epoch 24/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0151 - mse: 0.0151 Epoch 25/30 638/638 [==============================] - 1s 999us/step - loss: 0.0150 - mse: 0.0150 Epoch 26/30 638/638 [==============================] - 1s 998us/step - loss: 0.0148 - mse: 0.0148 Epoch 27/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0148 - mse: 0.0148 Epoch 28/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0147 - mse: 0.0147 Epoch 29/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0144 - mse: 0.0144 Epoch 30/30 638/638 [==============================] - 1s 1ms/step - loss: 0.0145 - mse: 0.0145 Training history across epochs for fold 1
78/78 [==============================] - 0s 919us/step 78/78 [==============================] - 0s 609us/step Vizualization for FDC for training fold (shown in dark hue) 1and predicted clusters from neural network on testing fold (shown in corresponding light hues) 1
Average percentage of patients belongs to the same cluster is: 92.59280085336647% Epoch 1/30 636/636 [==============================] - 1s 958us/step - loss: 0.7368 - mse: 0.7368 Epoch 2/30 636/636 [==============================] - 1s 972us/step - loss: 0.4379 - mse: 0.4379 Epoch 3/30 636/636 [==============================] - 1s 959us/step - loss: 0.3580 - mse: 0.3580 Epoch 4/30 636/636 [==============================] - 1s 975us/step - loss: 0.3246 - mse: 0.3246 Epoch 5/30 636/636 [==============================] - 1s 960us/step - loss: 0.3044 - mse: 0.3044 Epoch 6/30 636/636 [==============================] - 1s 971us/step - loss: 0.2908 - mse: 0.2908 Epoch 7/30 636/636 [==============================] - 1s 971us/step - loss: 0.2831 - mse: 0.2831 Epoch 8/30 636/636 [==============================] - 1s 978us/step - loss: 0.2766 - mse: 0.2766 Epoch 9/30 636/636 [==============================] - 1s 958us/step - loss: 0.2712 - mse: 0.2712 Epoch 10/30 636/636 [==============================] - 1s 954us/step - loss: 0.2668 - mse: 0.2668 Epoch 11/30 636/636 [==============================] - 1s 980us/step - loss: 0.2624 - mse: 0.2624 Epoch 12/30 636/636 [==============================] - 1s 968us/step - loss: 0.2572 - mse: 0.2572 Epoch 13/30 636/636 [==============================] - 1s 957us/step - loss: 0.2514 - mse: 0.2514 Epoch 14/30 636/636 [==============================] - 1s 964us/step - loss: 0.2461 - mse: 0.2461 Epoch 15/30 636/636 [==============================] - 1s 1ms/step - loss: 0.2405 - mse: 0.2405 Epoch 16/30 636/636 [==============================] - 1s 1000us/step - loss: 0.2355 - mse: 0.2355 Epoch 17/30 636/636 [==============================] - 1s 966us/step - loss: 0.2316 - mse: 0.2316 Epoch 18/30 636/636 [==============================] - 1s 964us/step - loss: 0.2271 - mse: 0.2271 Epoch 19/30 636/636 [==============================] - 1s 971us/step - loss: 0.2235 - mse: 0.2235 Epoch 20/30 636/636 [==============================] - 1s 962us/step - loss: 0.2200 - mse: 0.2200 Epoch 21/30 636/636 [==============================] - 1s 956us/step - loss: 0.2170 - mse: 0.2170 Epoch 22/30 636/636 [==============================] - 1s 961us/step - loss: 0.2148 - mse: 0.2148 Epoch 23/30 636/636 [==============================] - 1s 965us/step - loss: 0.2119 - mse: 0.2119 Epoch 24/30 636/636 [==============================] - 1s 963us/step - loss: 0.2083 - mse: 0.2083 Epoch 25/30 636/636 [==============================] - 1s 954us/step - loss: 0.2046 - mse: 0.2046 Epoch 26/30 636/636 [==============================] - 1s 983us/step - loss: 0.2013 - mse: 0.2013 Epoch 27/30 636/636 [==============================] - 1s 961us/step - loss: 0.1980 - mse: 0.1980 Epoch 28/30 636/636 [==============================] - 1s 966us/step - loss: 0.1945 - mse: 0.1945 Epoch 29/30 636/636 [==============================] - 1s 953us/step - loss: 0.1892 - mse: 0.1892 Epoch 30/30 636/636 [==============================] - 1s 975us/step - loss: 0.1867 - mse: 0.1867 Training history across epochs for fold 2
Epoch 1/30 636/636 [==============================] - 1s 942us/step - loss: 0.0803 - mse: 0.0803 Epoch 2/30 636/636 [==============================] - 1s 982us/step - loss: 0.0317 - mse: 0.0317 Epoch 3/30 636/636 [==============================] - 1s 964us/step - loss: 0.0262 - mse: 0.0262 Epoch 4/30 636/636 [==============================] - 1s 974us/step - loss: 0.0238 - mse: 0.0238 Epoch 5/30 636/636 [==============================] - 1s 939us/step - loss: 0.0224 - mse: 0.0224 Epoch 6/30 636/636 [==============================] - 1s 1ms/step - loss: 0.0215 - mse: 0.0215 Epoch 7/30 636/636 [==============================] - 1s 1ms/step - loss: 0.0207 - mse: 0.0207 Epoch 8/30 636/636 [==============================] - 1s 989us/step - loss: 0.0203 - mse: 0.0203 Epoch 9/30 636/636 [==============================] - 1s 982us/step - loss: 0.0193 - mse: 0.0193 Epoch 10/30 636/636 [==============================] - 1s 940us/step - loss: 0.0190 - mse: 0.0190 Epoch 11/30 636/636 [==============================] - 1s 952us/step - loss: 0.0191 - mse: 0.0191 Epoch 12/30 636/636 [==============================] - 1s 964us/step - loss: 0.0184 - mse: 0.0184 Epoch 13/30 636/636 [==============================] - 1s 973us/step - loss: 0.0181 - mse: 0.0181 Epoch 14/30 636/636 [==============================] - 1s 1ms/step - loss: 0.0176 - mse: 0.0176 Epoch 15/30 636/636 [==============================] - 1s 1ms/step - loss: 0.0173 - mse: 0.0173 Epoch 16/30 636/636 [==============================] - 1s 978us/step - loss: 0.0171 - mse: 0.0171 Epoch 17/30 636/636 [==============================] - 1s 1ms/step - loss: 0.0167 - mse: 0.0167 Epoch 18/30 636/636 [==============================] - 1s 1ms/step - loss: 0.0165 - mse: 0.0165 Epoch 19/30 636/636 [==============================] - 1s 1ms/step - loss: 0.0162 - mse: 0.0162 Epoch 20/30 636/636 [==============================] - 1s 1ms/step - loss: 0.0163 - mse: 0.0163 Epoch 21/30 636/636 [==============================] - 1s 1ms/step - loss: 0.0157 - mse: 0.0157 Epoch 22/30 636/636 [==============================] - 1s 1ms/step - loss: 0.0157 - mse: 0.0157 Epoch 23/30 636/636 [==============================] - 1s 973us/step - loss: 0.0151 - mse: 0.0151 Epoch 24/30 636/636 [==============================] - 1s 999us/step - loss: 0.0153 - mse: 0.0153 Epoch 25/30 636/636 [==============================] - 1s 973us/step - loss: 0.0152 - mse: 0.0152 Epoch 26/30 636/636 [==============================] - 1s 968us/step - loss: 0.0147 - mse: 0.0147 Epoch 27/30 636/636 [==============================] - 1s 984us/step - loss: 0.0151 - mse: 0.0151 Epoch 28/30 636/636 [==============================] - 1s 987us/step - loss: 0.0150 - mse: 0.0150 Epoch 29/30 636/636 [==============================] - 1s 953us/step - loss: 0.0148 - mse: 0.0148 Epoch 30/30 636/636 [==============================] - 1s 998us/step - loss: 0.0143 - mse: 0.0143 Training history across epochs for fold 2
79/79 [==============================] - 0s 745us/step 79/79 [==============================] - 0s 729us/step Vizualization for FDC for training fold (shown in dark hue) 2and predicted clusters from neural network on testing fold (shown in corresponding light hues) 2
Average percentage of patients belongs to the same cluster is: 91.47076946355948% Epoch 1/30 625/625 [==============================] - 1s 1ms/step - loss: 0.7316 - mse: 0.7316 Epoch 2/30 625/625 [==============================] - 1s 1ms/step - loss: 0.4436 - mse: 0.4436 Epoch 3/30 625/625 [==============================] - 1s 1ms/step - loss: 0.3615 - mse: 0.3615 Epoch 4/30 625/625 [==============================] - 1s 999us/step - loss: 0.3260 - mse: 0.3260 Epoch 5/30 625/625 [==============================] - 1s 1ms/step - loss: 0.3036 - mse: 0.3036 Epoch 6/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2902 - mse: 0.2902 Epoch 7/30 625/625 [==============================] - 1s 980us/step - loss: 0.2816 - mse: 0.2816 Epoch 8/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2749 - mse: 0.2749 Epoch 9/30 625/625 [==============================] - 1s 982us/step - loss: 0.2710 - mse: 0.2710 Epoch 10/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2663 - mse: 0.2663 Epoch 11/30 625/625 [==============================] - 1s 998us/step - loss: 0.2629 - mse: 0.2629 Epoch 12/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2577 - mse: 0.2577 Epoch 13/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2523 - mse: 0.2523 Epoch 14/30 625/625 [==============================] - 1s 987us/step - loss: 0.2459 - mse: 0.2459 Epoch 15/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2410 - mse: 0.2410 Epoch 16/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2363 - mse: 0.2363 Epoch 17/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2309 - mse: 0.2309 Epoch 18/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2261 - mse: 0.2261 Epoch 19/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2232 - mse: 0.2232 Epoch 20/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2183 - mse: 0.2183 Epoch 21/30 625/625 [==============================] - 1s 992us/step - loss: 0.2145 - mse: 0.2145 Epoch 22/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2108 - mse: 0.2108 Epoch 23/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2063 - mse: 0.2063 Epoch 24/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2032 - mse: 0.2032 Epoch 25/30 625/625 [==============================] - 1s 1ms/step - loss: 0.2006 - mse: 0.2006 Epoch 26/30 625/625 [==============================] - 1s 1ms/step - loss: 0.1953 - mse: 0.1953 Epoch 27/30 625/625 [==============================] - 1s 1ms/step - loss: 0.1913 - mse: 0.1913 Epoch 28/30 625/625 [==============================] - 1s 1ms/step - loss: 0.1883 - mse: 0.1883 Epoch 29/30 625/625 [==============================] - 1s 1ms/step - loss: 0.1852 - mse: 0.1852 Epoch 30/30 625/625 [==============================] - 1s 1ms/step - loss: 0.1820 - mse: 0.1820 Training history across epochs for fold 3
Epoch 1/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0825 - mse: 0.0825 Epoch 2/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0316 - mse: 0.0316 Epoch 3/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0255 - mse: 0.0255 Epoch 4/30 625/625 [==============================] - 1s 964us/step - loss: 0.0230 - mse: 0.0230 Epoch 5/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0216 - mse: 0.0216 Epoch 6/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0210 - mse: 0.0210 Epoch 7/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0205 - mse: 0.0205 Epoch 8/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0196 - mse: 0.0196 Epoch 9/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0194 - mse: 0.0194 Epoch 10/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0189 - mse: 0.0189 Epoch 11/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0187 - mse: 0.0187 Epoch 12/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0183 - mse: 0.0183 Epoch 13/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0181 - mse: 0.0181 Epoch 14/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0180 - mse: 0.0180 Epoch 15/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0176 - mse: 0.0176 Epoch 16/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0173 - mse: 0.0173 Epoch 17/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0174 - mse: 0.0174 Epoch 18/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0169 - mse: 0.0169 Epoch 19/30 625/625 [==============================] - 1s 981us/step - loss: 0.0169 - mse: 0.0169 Epoch 20/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0168 - mse: 0.0168 Epoch 21/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0166 - mse: 0.0166 Epoch 22/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0164 - mse: 0.0164 Epoch 23/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0163 - mse: 0.0163 Epoch 24/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0160 - mse: 0.0160 Epoch 25/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0159 - mse: 0.0159 Epoch 26/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0158 - mse: 0.0158 Epoch 27/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0155 - mse: 0.0155 Epoch 28/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0156 - mse: 0.0156 Epoch 29/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0149 - mse: 0.0149 Epoch 30/30 625/625 [==============================] - 1s 1ms/step - loss: 0.0152 - mse: 0.0152 Training history across epochs for fold 3
82/82 [==============================] - 0s 771us/step 82/82 [==============================] - 0s 771us/step Vizualization for FDC for training fold (shown in dark hue) 3and predicted clusters from neural network on testing fold (shown in corresponding light hues) 3
Average percentage of patients belongs to the same cluster is: 90.75880333399769%
print('Average percentage of patients belonging to the same cluster over all three folds:', np.mean(np.array(fold_readings)))
Average percentage of patients belonging to the same cluster over all three folds: 91.6074578836412
np.random.seed(42)
FDC_emb_five_data=entire_data_FDC_emb_five.loc[list(data.index)] #5D FDC embedding of training fold from entire data
FDC_emb_two_data=entire_data_FDC_emb_two.loc[list(data.index)] #2D embedding of training fold from entire data
FDC_emb_five_data.columns=colnames
#Thirty dimensional data of training fold as features_matrix(X_train)
features_matrix=np.array(data.drop(cluster_column_names, axis=1,inplace=False)) #X_train
#Five dimensional FDC embedding of training fold as target_matrix(y_train)
target_matrix=np.array(FDC_emb_five_data) #y_train
#Train a neural network to get five dimensional embedding
model_1=neural_network(len(features_matrix[0]),int(0.6*len(features_matrix[0])),int(0.36*len(features_matrix[0])),len(target_matrix[0]),"relu","sigmoid","mse")
history=model_1.fit(features_matrix,target_matrix,epochs=30,batch_size=8)
print('\n')
print('Training history across epochs for training data ')
plt.plot(history.history['mse'],'r')
plt.ylabel('mse')
plt.xlabel('epoch')
plt.show()
#Using same thirty dimensional features_matrix(X_train) from first neural network and encoded cluster labels of training fold as target_labels_matrix(y_train)
target_labels_matrix=np.array(data.loc[:,cluster_column_names]) #y
#Train a neural network to get encoded cluster labels
model_2=neural_network(len(features_matrix[0]),int(0.6*len(features_matrix[0])),int(0.36*len(features_matrix[0])),len(target_labels_matrix[0]),"relu","softmax","mse")
history=model_2.fit(features_matrix,target_labels_matrix,epochs=30,batch_size=8)
print('\n')
print('Training history across epochs for training data ')
plt.plot(history.history['mse'],'r')
plt.ylabel('mse')
plt.xlabel('epoch')
plt.show()
#Decoding cluster labels of training fold
decoded_target_labels_matrix=label_decoder(target_labels_matrix)
#Actual encoded cluster labels of validation data for metric calculation
ref_clusters=data_val.loc[:,cluster_column_names]
#Decoding encoded cluster labels of validation data
decoded_ref_clusters=label_decoder(ref_clusters)
#predicting validation data to get five dim embedding using trained model_1
validation_data=data_val.drop(cluster_column_names, axis=1,inplace=False)
predicted_5dim=pd.DataFrame(model_1.predict(validation_data), columns=colnames)
#UMAP on predicted 5D embedding
predicted_2dim=feature_clustering(30,0.01, "euclidean", predicted_5dim, 0)
#predicting validation data to get encoded cluster labels using trained model_2
predicted_clusters=pd.DataFrame(model_2.predict(validation_data))
#Decoding predicted encoded cluster labels
decoded_predicted_clusters=label_decoder(predicted_clusters)
#concatinating training and predicted 5D embedding
concatenated_5dim=pd.concat([FDC_emb_five_data,predicted_5dim])
#UMAP on concatinated embedding
two_dim_viz=feature_clustering(30, 0.01, 'euclidean', concatenated_5dim, 0)
#Concatinating decoded cluster labels of training data and predicted validation data
concatenated_cluster_labels=np.concatenate([np.array(decoded_target_labels_matrix),np.array(decoded_predicted_clusters)+len(np.unique(decoded_target_labels_matrix))])
two_dim_viz['Cluster']= concatenated_cluster_labels
#Setting dark colors for training data
darkerhues=['lightcoral','cornflowerblue','orange','mediumorchid', 'lightseagreen','olive', 'chocolate','steelblue']
colors_set2=[]
for i in range(len(np.unique(decoded_target_labels_matrix))):
colors_set2.append(darkerhues[i])
#Concatinating dark colors for training data and corresponding light colors for validation data
colors_set2=colors_set2+["lightpink", 'skyblue', 'wheat', "plum","paleturquoise", "lightgreen", 'burlywood','lightsteelblue']
print('Vizualization for FDC for training data (shown in dark hue) '+ 'and predicted clusters from neural network on validation data (shown in corresponding light hues) ')
#visualizing the clusters of both training and validation data
sns.lmplot( x="UMAP_0", y="UMAP_1", data=two_dim_viz, fit_reg=False, legend=False, hue='Cluster', scatter_kws={"s": 3},palette=sns.set_palette(sns.color_palette(colors_set2)))
plt.show()
#Metric calculation
CIM_predicted=cluster_incidence_matrix_mod(np.array(decoded_predicted_clusters))#Cluster incidence metric for predicted clusters
CIM_reference=cluster_incidence_matrix_mod(np.array(decoded_ref_clusters))#Cluster incidence metric for reference clusters
Product=np.dot(CIM_predicted,CIM_reference)
cluster_incidences_in_data=np.sum(CIM_reference,axis=1)
mean_points_in_same_clusters=np.mean(np.diagonal(Product)/cluster_incidences_in_data)
fold_readings.append(mean_points_in_same_clusters*100)
print("Average percentage of patients belongs to the same cluster is: {}%".format(mean_points_in_same_clusters*100))
print('\n')
print('\n')
print('\n')
Epoch 1/30 950/950 [==============================] - 1s 1ms/step - loss: 0.6432 - mse: 0.6432 Epoch 2/30 950/950 [==============================] - 1s 1ms/step - loss: 0.3759 - mse: 0.3759 Epoch 3/30 950/950 [==============================] - 1s 1ms/step - loss: 0.3215 - mse: 0.3215 Epoch 4/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2956 - mse: 0.2956 Epoch 5/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2807 - mse: 0.2807 Epoch 6/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2717 - mse: 0.2717 Epoch 7/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2631 - mse: 0.2631 Epoch 8/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2566 - mse: 0.2566 Epoch 9/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2506 - mse: 0.2506 Epoch 10/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2448 - mse: 0.2448 Epoch 11/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2409 - mse: 0.2409 Epoch 12/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2372 - mse: 0.2372 Epoch 13/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2347 - mse: 0.2347 Epoch 14/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2319 - mse: 0.2319 Epoch 15/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2288 - mse: 0.2288 Epoch 16/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2269 - mse: 0.2269 Epoch 17/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2243 - mse: 0.2243 Epoch 18/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2218 - mse: 0.2218 Epoch 19/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2191 - mse: 0.2191 Epoch 20/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2159 - mse: 0.2159 Epoch 21/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2127 - mse: 0.2127 Epoch 22/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2088 - mse: 0.2088 Epoch 23/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2049 - mse: 0.2049 Epoch 24/30 950/950 [==============================] - 1s 1ms/step - loss: 0.2009 - mse: 0.2009 Epoch 25/30 950/950 [==============================] - 1s 1ms/step - loss: 0.1967 - mse: 0.1967 Epoch 26/30 950/950 [==============================] - 1s 1ms/step - loss: 0.1934 - mse: 0.1934 Epoch 27/30 950/950 [==============================] - 1s 1ms/step - loss: 0.1885 - mse: 0.1885 Epoch 28/30 950/950 [==============================] - 1s 1ms/step - loss: 0.1864 - mse: 0.1864 Epoch 29/30 950/950 [==============================] - 1s 1ms/step - loss: 0.1817 - mse: 0.1817 Epoch 30/30 950/950 [==============================] - 1s 1ms/step - loss: 0.1795 - mse: 0.1795 Training history across epochs for training data
Epoch 1/30 950/950 [==============================] - 2s 1ms/step - loss: 0.0662 - mse: 0.0662 Epoch 2/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0273 - mse: 0.0273 Epoch 3/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0232 - mse: 0.0232 Epoch 4/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0213 - mse: 0.0213 Epoch 5/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0204 - mse: 0.0204 Epoch 6/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0197 - mse: 0.0197 Epoch 7/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0187 - mse: 0.0187 Epoch 8/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0186 - mse: 0.0186 Epoch 9/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0177 - mse: 0.0177 Epoch 10/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0175 - mse: 0.0175 Epoch 11/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0172 - mse: 0.0172 Epoch 12/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0172 - mse: 0.0172 Epoch 13/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0168 - mse: 0.0168 Epoch 14/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0162 - mse: 0.0162 Epoch 15/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0159 - mse: 0.0159 Epoch 16/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0158 - mse: 0.0158 Epoch 17/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0157 - mse: 0.0157 Epoch 18/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0151 - mse: 0.0151 Epoch 19/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0149 - mse: 0.0149 Epoch 20/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0152 - mse: 0.0152 Epoch 21/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0149 - mse: 0.0149 Epoch 22/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0147 - mse: 0.0147 Epoch 23/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0145 - mse: 0.0145 Epoch 24/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0141 - mse: 0.0141 Epoch 25/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0139 - mse: 0.0139 Epoch 26/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0140 - mse: 0.0140 Epoch 27/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0138 - mse: 0.0138 Epoch 28/30 950/950 [==============================] - 1s 999us/step - loss: 0.0138 - mse: 0.0138 Epoch 29/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0136 - mse: 0.0136 Epoch 30/30 950/950 [==============================] - 1s 1ms/step - loss: 0.0132 - mse: 0.0132 Training history across epochs for training data
80/80 [==============================] - 0s 591us/step 80/80 [==============================] - 0s 701us/step Vizualization for FDC for training data (shown in dark hue) and predicted clusters from neural network on validation data (shown in corresponding light hues)
Average percentage of patients belongs to the same cluster is: 90.20616212811711%